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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgataattgtgtaacctttgcatctaatgcagcctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT

Basic information

species Vitis vinifera
transcript Vv12s0028g03090.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g48820.1 (Oryza sativa), 3'ss of exon 12
--gtattgata--attgtgtaacctttgcatctaatgcagc-ctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
   |   ||    ||     ||  ||    | |||       || |   | | |||| ||||||   |    | |||||||||||||  | ||||||||||||||||||||||| |||||||||||  ||||||| ||||||||||||  ||||||||| |||||||||||||| |
gtatgccgaccacatccaaaaaagttcaattgtaacctgttgctatcttattgattttgtttattgatctcttcagAAATCTGGACTGAGAGACCTTACAACAAGCAAGACACCTGAGGCATCTATATCTGCTGCACTGTCAAGGGATTCAAAGCTTTTCGAAAGGACTGCACCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g48180.1 (Oryza sativa), 3'ss of exon 11
------------------gtattga--taattgtgtaacctttgcatctaatgcagcctcttaaactcatttggttta---tattttatgta-agAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
                   |  |     |||| ||     |     |||  |      |||  |  | | |   ||||   | ||||||||  ||||||||||| |  | ||||| |||||||||||||| || ||||||||||| ||||||||| |||||||||||  ||| ||||||||  | ||||| || |
gtttgtttccacacagatatgctagctcaattttgctttgtgattttcttctttttgttctatagttgaatgaatttactcttttttatgtttagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACGCCTGAGGCATCTATAGCTGCTGCCTTGTCAAGGGATACAAAACTTTTTGAGCGAACTGCTCCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G159357_T01 (Zea mays), 3'ss of exon 12
----------------gtattgataattgtgtaacctttgcatctaatgcagcc-tcttaaactcatttggtt---tatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
                ||||   ||||    | ||| ||     ||| |  |   |||| || |   |  | |   ||| ||     | ||||||||||| |  | ||||| ||||||||||||||||| |||||||| || ||||||||| |||| ||||||  |||||||||||| || ||||| || |
gtacatacacatatatgtatctttaatccctttacccttctccttaaagtggttatcttcaattttgtaagctgattattttcctgttcagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACACCTGAGGCATCCATAGCTGCTGCCTTGTCTAGGGATACAAAGCTTTTTGAGAGAACTGCTCCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G125294_T01 (Zea mays), 3'ss of exon 12
-----------------gtattgata-attgtg-taacct-ttgcatctaatgcagcctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
                   |||  || |||||  | |||| ||   ||||||| | | | |   | |  |||| |   | |||    | |||||||||||||| | |||||||||||||| ||||||||||||||||||||  |||| ||  |||| || ||    |||||||||||||| || ||||| |
gtatatccgcatcaaataaatttctagattgtactgacctgttatttctaatggaacatat---attggtttgttccttttttgtcttcagAAATCTGGACTTAGAGACCTTACAACAAGTAAGACACCAGAGGCATCTATATCTGCGGCATTGTCGAGAGACACTAAGCTTTTTGAAAGAACGGCACCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AC196465.3_FGT006 (Zea mays), 3'ss of exon 6
----------gtattgataattgtgtaacctttgcatctaatgcagcc-tcttaaactcatttggt---ttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
           |||    ||        |    ||  |||| |  |   |||| || |   |  |    |||| ||     | ||||||||||| |  | ||||| ||||||||||||||||| |||||||| || ||||||||  |||| ||||||| ||| |||||||| || ||||| || |
gtacacatatatatcctgaacccccctcctcccgcccctaaagtggttatcttcaattttctaagctgattattttcctgttcagAAATCTGGATTGAGAGACCTCACAACAAGCAAGACACCTGAGGCATCCATAGCTGCTGCTTTGTCTAGGGATGCAAAACTTTTTGAGAGAACTGCTCCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G122750_T01 (Zea mays), 3'ss of exon 12
---------------------gtattgataattgtgtaacctttgcatctaatgcagcctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
                      | | |||   |    | |  ||   ||||||| | ||| |   |||  |||| | | | |||    | |||||||||||||  | |||||||||||||| |||||||||||||||||| |  |||| ||  |||| || ||    |||||||||||||| || ||||| |
gtatatctacatcaaacaaatttctagattgatactgacctgttatttctaatggaacctat---actggtttgttct-tgtttctcttcagAAATCTGGACTGAGAGACCTTACAACAAGTAAGACACCAGAGGCATCTGTATCTGCGGCATTGTCGAGAGACACTAAGCTTTTTGAAAGAACAGCACCTT

upper sequence: Vv12s0028g03090.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G44290.1 (Glycine max), 3'ss of exon 14
--------gtattgataattgtgtaacctttgcatctaatgcagcctcttaaactcatttggtttatattttatgta---agAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
         |  |  |   ||| | |    |  |||| |||       ||||| |   ||  ||| | |||| | ||   |||||||||||||||| || |||||||||||||| ||||||||||| |||||| |||||||  |||| ||||||  ||| || ||||||||||| || || |
gtataactattctactggatgtcttattcata-atctcatgttaatgattaaattttcttcattttt-ttttgtttatctagAAATCTGGACTTCGTGATCTTACAACAAGCAAAACACCAGAGGCTTCTATTTCTGCTGCTTTGTCTAGGGATACAAAACTATTTGAAAGGACAGCTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctttgcatctaatgcagcctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT
         atctaat  putative branch site (score: 3)
                                atttggtttatatttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgataattgtgtaacctttgcatctaatgcagcctcttaaactcatttggtttatattttatgtaagAAATCTGGACTTCGGGACCTTACAACAAGCAAGACACCAGAGGCATCTATTGCTGCTGCCCTGTCAAGGGATGGAAAGCTTTTTGAAAGGACTGCACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA